Robust Variance Score (RVS) test for association of variants from next generation sequence data with binary traits using external controls

calc_centralize_matrix | Function to centralize a matrix X by column |

calc_EG | Function to calculate the conditional expected genotype... |

calc_EG_general | More general function to calculate the conditional expected... |

calc_EG_Var | Function to calculate the variance of conditional expected... |

calc_EG_Var_general | Function to calculate the variance of conditional expected... |

calc_EM | Function to use EM algorithm to estimate the genotype... |

calc_Mr | Function to calcualte likelihood P(D|G) for simulating data,... |

calc_pobs_ndepth | Function to calculate the likelihood matrix P(D|G) given a... |

calc_psingle | Function to compute the genotype likelihood of a read given... |

calc_robust_Var | Function to calcualte the robust variance of E(Gij|Dij) for... |

calc_score_test | Function to calculate the score test for given expected... |

calc_score_test1 | clac_score_test1 calculates the score test for given expected... |

calc_ScoreV | calc_ScoreV gets score vector S for nsnp number of rare... |

calc_ScoreV_likely | calc_ScoreV_likely: Get Variance of vector S by likelihood... |

calc_ScoreV_regVar | calc_ScoreV_regVar: Get Variance of vector S by regular... |

calc_ScoreV_RVS | calc_ScoreV_RVS calculates variance of vector S by RVS using... |

calc_simu_exp | Function to calculate expected genotype data for simuation... |

check_hom_matrix | Function to remove the homozygosity of a rare SNP in case or... |

clist | clist can combine two lists with the same structure. |

combine_twogeno | Function to combine two sets of ped pairs for two samples |

common_coord | Function to find the variants presenting in two datasets. |

convert | convert two columns of a variant from ped file into additive... |

cor.X.function | Function to edit the correlation matrix of expected genotype... |

filter_by_miss | Function to filter out variants by missing rate p |

filter_genocall | Function to filter out variants in the genotype hard call... |

filter_VCF_SNPs | Function to filter variants in VCF files based on column 2... |

generate_seq_1ind | Generate sequence data for one indiviudal with read depth rd... |

generate_seqdata_1var | Generate sequence data for ncase and ncontrol indiviudal at... |

generate_seqdata_OR | Function to simulate data for one variant by given parameters |

generate_seqdata_OR1 | Function to simulate data for one variant by given parameters |

geno_add_2pheno | Function to add the phenotype in the 6th column of the... |

geno_process | Function to deal with genotype hard call files in additive... |

get_allele_frq | Function to calculate the allele frequency from additive... |

get_exp_geno | Function to generates the expected probabilities of the... |

get_exp_MAF | Function to calculate the minor allele frequency (MAF) from... |

get_IDs | Function to seprates the case and control IDs. |

get_likelihood_vcf | Function to get Likelihoods for all possible genotypes given... |

get_lsingle_vcf | Function to parse Phred-scaled likelihoods |

minor_allele | Function to find the minor allele in the whole sample |

odds.2.probs | Function to calculate the probability from given odds |

ped_2_additive | Function to combine two ped files for case and controls and... |

rbindlist | rbindlist can rbind combine two lists with the same... |

regScore_perm | Use regular Score/Trend test for association for given... |

regScore_Rao | Use regular Score/Trend test for association for given... |

regScore_rare | It calls functions... |

regScore_rare1 | It calls functions... |

reset_minor_additive | Function to reset the additive coding genotype into nubmer of... |

RVS_asy | RVS using asymptotic distribution for score test statistic |

RVS_btrap | use RVS to test associaton by bootrtrap, given phenotype (Y),... |

RVS_rare | It calls functions... |

RVS_rare1 | It calls functions... |

RVS_rare2 | It calls functions... |

sample_bootstrap | Function to bootstrap sampling |

seq_call | Function to produce a sequencing read at one locus with... |

seqdata_nvar | Generate sequence data for nsnp variants |

seq_eg_freq | use the simulated data to calculate the expected genotype... |

sim.corr.binary.data | Function to simulate the correlated binary data with given... |

snp_true_2T | Function to change all TRUE genotype into T |

subset_ind | Function to take a subset the samples from a larger genotype... |

subset_snp | Function to extract the genotype columns for chosen variants... |

test_Calpha | Function to obtain p-value by Calpha method (quadratic test)... |

test_CAST | Function to obtain p-value by CAST method (linear test) for J... |

test_Hotelling | Function to obtain pvalue by Hotelling test for J number of... |

vcf_process | the main function to call the VCF file and return the... |

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